1 Setup

setwd("/mnt/picea/projects/arabidopsis/jhanson/arabidopsis-nutrition-TOR/Conditions")
suppressPackageStartupMessages({
    library(data.table)
    library(DESeq2)
    library(gplots)
    library(here)
    library(hyperSpec)
    library(limma)
    library(LSD)
    library(magrittr)
    library(matrixStats)
    library(parallel)
    library(pander)
    library(plotly)
    library(RColorBrewer)
    library(scatterplot3d)
    library(tidyverse)
    library(tximport)
    library(VennDiagram)
    library(vsn)
})
suppressPackageStartupMessages({
    source("~/Git/UPSCb/UPSCb-common/src/R/featureSelection.R")
    source("~/Git/UPSCb/UPSCb-common/src/R/gopher.R")
    source("~/Git/UPSCb/UPSCb-common/src/R/plot.multidensity.R")
    source("~/Git/UPSCb/UPSCb-common/src/R/volcanoPlot.R")
})
lfc <- 0.5
FDR <- 0.01
pal <- c(brewer.pal(8,"Dark2"),1)
pal2 <- brewer.pal(9,"Paired") #require package RColorBrewer
cols <- rainbow(17)
hpal <- colorRampPalette(c("blue","white","red"))(100)
mar <- par("mar")

2 Raw data

2.1 Prepare the sample list

  • Read the sample information
samples <- read.csv("~/Git/arabidopsis-nutrition-tor/doc/samples3.csv")
samples$Nutrition <- as.factor(samples$Nutrition)
samples$AZD <- as.factor(samples$AZD)
  • Remove unnecessary samples
samples %<>% filter(!grepl("P11554_1",SciLifeID)) %>% 
    filter(! SciLifeID %in% c("P13406_101",
                        "P14066_128",
                        "P14066_133",
                        "P13406_102",
                        "P14066_131")) %>%
    filter(! Nutrition == "PKS") %>%
    mutate(Nutrition,Nutrition=relevel(Nutrition,"NPS")) %>% 
    mutate(AZD,AZD=relevel(AZD,"DMSO"))

samples <- samples[order(samples$Timepoint, samples$Nutrition, samples$AZD),]

samples %<>% mutate(Timepoint,Timepoint=factor(paste0("T",Timepoint)))

2.2 Load the data

  • Call the data
filenames <- list.files("../Salmon", 
                    recursive = TRUE, 
                    pattern = "quant.sf",
                    full.names = TRUE)
  • Name the data
names(filenames) <- sub("_S.*","",sapply(strsplit(filenames, "/"), .subset, 3))
  • Match data <=> sample list
filenames <- filenames[match(samples$SciLifeID,names(filenames))]
filenames <-filenames[!is.na(names(filenames))]
samples <- samples[match(names(filenames),samples$SciLifeID),]
  • Annotate the samples
samples$Conditions <- factor(paste(samples$Timepoint,
                                   samples$Nutrition,
                                   samples$AZD,sep="_"),
                             levels=c("T0_T0_0",
                                      "T6_NPS_DMSO", "T6_NPS_AZD", "T6_NS_DMSO", "T6_NS_AZD", "T6_NP_DMSO", "T6_NP_AZD",
                                      "T24_NPS_DMSO", "T24_NPS_AZD", "T24_NS_DMSO", "T24_NS_AZD", "T24_NP_DMSO", "T24_NP_AZD"))
samples$Batch <- factor(substr(samples$SciLifeID,1,8))
samples <- cbind(samples,
                 Id = gsub(".+-",
                           "",
                           samples$SampleName))
samples <- cbind(samples,
                 Tp_Id = factor(paste(samples$Timepoint,
                                      samples$Id,
                                      sep=".")))
write.csv(samples,"/mnt/picea/projects/arabidopsis/jhanson/arabidopsis-nutrition-TOR/analysis_Tom/samplelist.csv")

3 Expression data

3.1 Calculate the expression values

  • Read the expression at the transcript level
tx <- suppressMessages(tximport(files = filenames, 
                                type = "salmon", 
                                txOut = TRUE))
  • Summarize to genes
tx2gene <- data.frame(TXID=rownames(tx$counts),
                      GENEID=sub("\\.[0-9]+","",rownames(tx$counts)))
gx <- summarizeToGene(tx,tx2gene=tx2gene)
## summarizing abundance
## summarizing counts
## summarizing length
kg <- round(gx$counts) 
  • Sanity check
stopifnot(all(colnames(kg) == samples$SciLifeID))

3.2 Raw data export

#dir.create(file.path("analysis_Tom","salmon"),showWarnings=FALSE,recursive=TRUE)
#write.table(kg,file="/mnt/picea/projects/arabidopsis/jhanson/arabidopsis-nutrition-TOR/analysis_Tom/nutrition-unormalised-gene-expression_data.csv")
#save(kg, samples, file = "/mnt/picea/projects/arabidopsis/jhanson/arabidopsis-nutrition-TOR/analysis_Tom/counts.rda")

3.3 Preliminary validations

  • Check for the genes that are never expressed
sel <- rowSums(kg) == 0 
sprintf("%s%% (%s) of %s genes are not expressed",
        round(sum(sel) * 100/ nrow(kg),digits=1),
        sum(sel),
        nrow(kg))
## [1] "17.9% (5793) of 32310 genes are not expressed"

4 Data normalization and biological quality control

For visualization, the data is submitted to a variance stabilization transformation using DESeq2. The dispersion is estimated independently of the sample type

dds <- DESeqDataSetFromMatrix(
    countData = kg,
    colData = samples,
    design = ~ Conditions)
## converting counts to integer mode
dds <- estimateSizeFactors(dds)

4.1 Perform a Variance Stabilizing Transformation for plotting

vst <- varianceStabilizingTransformation(dds,blind=FALSE)
vsd <- assay(vst)
vsd <- vsd - min(vsd)
  • Write out
stopifnot(all(colnames(vsd) == samples$SciLifeID))
colnames(vsd) <- samples$Tp_Id
write.csv(vsd,"/mnt/picea/projects/arabidopsis/jhanson/arabidopsis-nutrition-TOR/analysis_Tom/library-size-normalized_variance-stabilized_data_nutrition.csv")

4.2 Multivariate analysis by PCA

Principal Component Analysis on the normalized data * Establishment of the PCA

conditions1 <- factor(paste(samples$AZD,samples$Nutrition,sep="_"))
pc <- prcomp(t(vsd))
percent <- round(summary(pc)$importance[2,]*100);percent
##  PC1  PC2  PC3  PC4  PC5  PC6  PC7  PC8  PC9 PC10 PC11 PC12 PC13 PC14 PC15 PC16 
##   43   24   13    6    4    2    1    1    1    1    0    0    0    0    0    0 
## PC17 PC18 PC19 PC20 PC21 PC22 PC23 PC24 PC25 PC26 PC27 PC28 PC29 PC30 PC31 PC32 
##    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
## PC33 PC34 PC35 PC36 PC37 PC38 PC39 PC40 PC41 PC42 PC43 PC44 
##    0    0    0    0    0    0    0    0    0    0    0    0
  • Graphical representation of PC1 x PC2
conds <- droplevels(conditions1)
plot(pc$x[,1],
     pc$x[,2],
     xlab=paste("Comp. 1 (",percent[1],"%)",sep=""),
     ylab=paste("Comp. 2 (",percent[2],"%)",sep=""),
     col=pal[as.integer(conds)],
     pch=c(15,16,17)[as.factor(samples$Timepoint)],
     main="All timepoints")

legend("bottomright",pch=19,
       col=pal[1:nlevels(conds)],
       legend=levels(conds))

legend("topleft",pch=c(15,16,17),
       col="black",
       legend=c("T0","T6","T24"))

  • Graphical representation of PC2 x PC3
plot(pc$x[,2],
     pc$x[,3],
     xlab=paste("Comp. 2 (",percent[2],"%)",sep=""),
     ylab=paste("Comp. 3 (",percent[3],"%)",sep=""),
     col=pal[as.integer(conds)],
     pch=c(15,16,17)[as.factor(samples$Timepoint)],
     main="All timepoints")

legend("topleft",pch=19,
       col=pal[1:nlevels(conds)],
       legend=levels(conds))

legend("bottomleft",pch=c(15,16,17),
       col="black",
       legend=c("T0","T6","T24"))

  • Graphical representation of PC1 x PC3
plot(pc$x[,1],
     pc$x[,3],
     xlab=paste("Comp. 1 (",percent[1],"%)",sep=""),
     ylab=paste("Comp. 3 (",percent[3],"%)",sep=""),
     col=pal[as.integer(conds)],
     pch=c(15,16,17)[as.factor(samples$Timepoint)],
     main="All timepoints")

legend("bottomleft",pch=19,
       col=pal[1:nlevels(conds)],
       legend=levels(conds))

legend("bottomright",pch=c(15,16,17),
       col="black",
       legend=c("T0","T6","T24"))

5 Differential expression compared to T0

5.1 Filtration of samples based on timepoint

sel <- samples$Timepoint %in% c("T0","T6","T24")
suppressMessages(dds <- DESeqDataSetFromMatrix(
    countData = kg[,sel],
    colData = samples[sel,],
    design = ~ Conditions))

5.2 Differential expression analysis

dds <- DESeq(dds)
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 2 genes
## -- DESeq argument 'minReplicatesForReplace' = 7 
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing

5.3 Variance Stabilizing Transformation and DEG lists

5.3.1 Perform a Variance Stabilizing Transformation for plotting

vst <- varianceStabilizingTransformation(dds,blind=FALSE)
vsd <- assay(vst)
vsd <- vsd - min(vsd)

The contrast by default is the first one (not Intercept)

resultsNames(dds)
##  [1] "Intercept"                          "Conditions_T6_NPS_DMSO_vs_T0_T0_0" 
##  [3] "Conditions_T6_NPS_AZD_vs_T0_T0_0"   "Conditions_T6_NS_DMSO_vs_T0_T0_0"  
##  [5] "Conditions_T6_NS_AZD_vs_T0_T0_0"    "Conditions_T6_NP_DMSO_vs_T0_T0_0"  
##  [7] "Conditions_T6_NP_AZD_vs_T0_T0_0"    "Conditions_T24_NPS_DMSO_vs_T0_T0_0"
##  [9] "Conditions_T24_NPS_AZD_vs_T0_T0_0"  "Conditions_T24_NS_DMSO_vs_T0_T0_0" 
## [11] "Conditions_T24_NS_AZD_vs_T0_T0_0"   "Conditions_T24_NP_DMSO_vs_T0_T0_0" 
## [13] "Conditions_T24_NP_AZD_vs_T0_T0_0"

5.3.2 Effect of 6 hrs of treatment

5.3.2.1 Effect of nutrition re-supply

res <- results(dds,name = "Conditions_T6_NPS_DMSO_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T6_NPS_DMSO_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 9664 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 5302 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 4362 genes that are repressed
NPS_DMSO_High_6hrs <- rownames(res[cutoff1,])
NPS_DMSO_Low_6hrs <- rownames(res[cutoff2,])

5.3.2.2 Effect of nutrition re-supply in presence of AZD

res <- results(dds,name = "Conditions_T6_NPS_AZD_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T6_NPS_AZD_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 8735 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 4639 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 4096 genes that are repressed
NPS_AZD_High_6hrs <- rownames(res[cutoff1,])
NPS_AZD_Low_6hrs <- rownames(res[cutoff2,])

5.3.2.3 Effect of nutrition re-supply in presence of phosphate limitation

res <- results(dds,name = "Conditions_T6_NS_DMSO_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T6_NS_DMSO_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 6589 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 3553 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 3036 genes that are repressed
NS_DMSO_High_6hrs <- rownames(res[cutoff1,])
NS_DMSO_Low_6hrs <- rownames(res[cutoff2,])

5.3.2.4 Effect of nutrition re-supply in presence of AZD and phosphate limitation

res <- results(dds,name = "Conditions_T6_NS_AZD_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T6_NS_AZD_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 9218 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 4775 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 4443 genes that are repressed
NS_AZD_High_6hrs <- rownames(res[cutoff1,])
NS_AZD_Low_6hrs <- rownames(res[cutoff2,])

5.3.2.5 Effect of nutrition re-supply in presence of sugar limitation

res <- results(dds,name = "Conditions_T6_NP_DMSO_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T6_NP_DMSO_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 9491 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 5053 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 4438 genes that are repressed
NP_DMSO_High_6hrs <- rownames(res[cutoff1,])
NP_DMSO_Low_6hrs <- rownames(res[cutoff2,])

5.3.2.6 Effect of nutrition re-supply in presence of AZD and sugar limitation

res <- results(dds,name = "Conditions_T6_NP_AZD_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T6_NP_AZD_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 7818 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 4332 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 3486 genes that are repressed
NP_AZD_High_6hrs <- rownames(res[cutoff1,])
NP_AZD_Low_6hrs <- rownames(res[cutoff2,])

5.3.3 Effect of 24 hrs of treatment

5.3.3.1 Effect of nutrition re-supply

res <- results(dds,name = "Conditions_T24_NPS_DMSO_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T24_NPS_DMSO_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 10531 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 5150 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 5381 genes that are repressed
NPS_DMSO_High_24hrs <- rownames(res[cutoff1,])
NPS_DMSO_Low_24hrs <- rownames(res[cutoff2,])

5.3.3.2 Effect of nutrition re-supply in presence of AZD

res <- results(dds,name = "Conditions_T24_NPS_AZD_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T24_NPS_AZD_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 8349 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 4066 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 4283 genes that are repressed
NPS_AZD_High_24hrs <- rownames(res[cutoff1,])
NPS_AZD_Low_24hrs <- rownames(res[cutoff2,])

5.3.3.3 Effect of nutrition re-supply in presence of phosphate limitation

res <- results(dds,name = "Conditions_T24_NS_DMSO_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T24_NS_DMSO_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 4579 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 2165 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 2414 genes that are repressed
NS_DMSO_High_24hrs <- rownames(res[cutoff1,])
NS_DMSO_Low_24hrs <- rownames(res[cutoff2,])

5.3.3.4 Effect of nutrition re-supply in presence of AZD and of phosphate limitation

res <- results(dds,name = "Conditions_T24_NS_AZD_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T24_NS_AZD_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 7102 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 3258 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 3844 genes that are repressed
NS_AZD_High_24hrs <- rownames(res[cutoff1,])
NS_AZD_Low_24hrs <- rownames(res[cutoff2,])

5.3.3.5 Effect of nutrition re-supply in presence of sugar limitation

res <- results(dds,name = "Conditions_T24_NP_DMSO_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T24_NP_DMSO_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 9502 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 4685 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 4817 genes that are repressed
NP_DMSO_High_24hrs <- rownames(res[cutoff1,])
NP_DMSO_Low_24hrs <- rownames(res[cutoff2,])

5.3.3.6 Effect of nutrition re-supply in presence of AZD and sugar limitation

res <- results(dds,name = "Conditions_T24_NP_AZD_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T24_NP_AZD_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 8906 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 4614 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 4292 genes that are repressed
NP_AZD_High_24hrs <- rownames(res[cutoff1,])
NP_AZD_Low_24hrs <- rownames(res[cutoff2,])

6 Differential expression based on the nutrition and treatment at T6

6.1 Filtration of samples based on timepoint

samples %<>% mutate(Conditions,Conditions=relevel(Conditions,"T6_NPS_DMSO"))
sel <- samples$Timepoint %in% c("T6")
suppressMessages(dds <- DESeqDataSetFromMatrix(
    countData = kg[,sel],
    colData = samples[sel,],
    design = ~ Conditions))

6.2 Differential expression analysis

dds <- DESeq(dds)
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing

6.3 Variance Stabilising Transformation

6.3.1 Perform a Variance Stabilizing Transformation for plotting

vst <- varianceStabilizingTransformation(dds,blind=FALSE)
vsd <- assay(vst)
vsd <- vsd - min(vsd)

6.4 Contrasts to NPS_DMSO at T6

The contrast by default is the first one (not Intercept)

resultsNames(dds)
## [1] "Intercept"                           
## [2] "Conditions_T6_NPS_AZD_vs_T6_NPS_DMSO"
## [3] "Conditions_T6_NS_DMSO_vs_T6_NPS_DMSO"
## [4] "Conditions_T6_NS_AZD_vs_T6_NPS_DMSO" 
## [5] "Conditions_T6_NP_DMSO_vs_T6_NPS_DMSO"
## [6] "Conditions_T6_NP_AZD_vs_T6_NPS_DMSO"

6.4.1 Nutrition effect of carbon starvation

6.4.1.1 Extraction of the results from the DESeq analysis

res <- results(dds,name = "Conditions_T6_NP_DMSO_vs_T6_NPS_DMSO")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T6_NP_DMSO_vs_T6_NPS_DMSO.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
SucEffect6hrs <- rownames(res[cutoffs,])
SucLow6hrs <- rownames(res[cutoff2,])
SucHigh6hrs <- rownames(res[cutoff1,])

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 1693 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 709 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 984 genes that are repressed

6.4.1.2 MA plot

DESeq2::plotMA(res)

6.4.1.3 Volcano plot

volcanoPlot(res, lfc = 1)

6.4.1.4 Heatmap

hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
                Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
                distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
                hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))

6.4.2 Nutrition effect of phosphorus starvation

6.4.2.1 Extraction of the results from the DESeq analysis

res <- results(dds,name = "Conditions_T6_NS_DMSO_vs_T6_NPS_DMSO")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T6_NS_DMSO_vs_T6_NPS_DMSO.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
PiEffect6hrs <- rownames(res[cutoffs,])
PiLow6hrs <- rownames(res[cutoff2,])
PiHigh6hrs <- rownames(res[cutoff1,])

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 6994 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 3173 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 3821 genes that are repressed

6.4.2.2 MA plot

DESeq2::plotMA(res)

6.4.2.3 Volcano plot

volcanoPlot(res, lfc=1)

6.4.2.4 Heatmap

hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
                Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
                distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
                hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))

6.4.3 Effect of AZD-8055

6.4.3.1 Extraction of the results from the DESeq analysis

res <- results(dds,name = "Conditions_T6_NPS_AZD_vs_T6_NPS_DMSO")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T6_NPS_AZD_vs_T6_NPS_DMSO.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
AzdEffect6hrs <- rownames(res[cutoffs,])
AzdLow6hrs <- rownames(res[cutoff2,])
AzdHigh6hrs <- rownames(res[cutoff1,])

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 6470 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 2866 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 3604 genes that are repressed

6.4.3.2 MA plot

DESeq2::plotMA(res)

6.4.3.3 Volcano plot

volcanoPlot(res, lfc=1)

6.4.3.4 Heatmap

hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
                Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
                distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
                hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))

6.4.4 Combined effect of AZD treatment and sugar starvation

6.4.4.1 Extraction of the results from the DESeq analysis

res <- results(dds,name = "Conditions_T6_NP_AZD_vs_T6_NPS_DMSO")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T6_NP_AZD_vs_T6_NPS_DMSO.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
AzdNP6hrs <- rownames(res[cutoffs,])
AzdNPLow6hrs <- rownames(res[cutoff2,])
AzdNPHigh6hrs <- rownames(res[cutoff1,])

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 6434 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 2939 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 3495 genes that are repressed

6.4.4.2 MA plot

DESeq2::plotMA(res)

6.4.4.3 Volcano plot

volcanoPlot(res, lfc=1)

6.4.4.4 Heatmap

hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
                Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
                distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
                hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))

6.4.5 Combined effect of AZD treatment and phosphorus starvation

6.4.5.1 Extraction of the results from the DESeq analysis

res <- results(dds,name = "Conditions_T6_NS_AZD_vs_T6_NPS_DMSO")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T6_NS_AZD_vs_T6_NPS_DMSO.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
AzdNS6hrs <- rownames(res[cutoffs,])
AzdNSLow6hrs <- rownames(res[cutoff2,])
AzdNSHigh6hrs <- rownames(res[cutoff1,])

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 9390 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 4556 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 4834 genes that are repressed

6.4.5.2 MA plot

DESeq2::plotMA(res)

6.4.5.3 Volcano plot

volcanoPlot(res, lfc=1)

6.4.5.4 Heatmap

hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
                Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
                distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
                hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))

7 Differential expression based on the nutrition and treatment at T24

7.1 Filtration of samples based on timepoint

samples %<>% mutate(Conditions,Conditions=relevel(Conditions,"T24_NPS_DMSO"))
sel <- samples$Timepoint %in% c("T24")
suppressMessages(dds <- DESeqDataSetFromMatrix(
    countData = kg[,sel],
    colData = samples[sel,],
    design = ~ Conditions))

7.2 Differential expression analysis

dds <- DESeq(dds)
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing

7.3 Variance Stabilising Transformation

7.3.1 Perform a Variance Stabilizing Transformation for plotting

vst <- varianceStabilizingTransformation(dds,blind=FALSE)
vsd <- assay(vst)
vsd <- vsd - min(vsd)

7.4 Contrasts to NPS_DMSO

The contrast by default is the first one (not Intercept)

resultsNames(dds)
## [1] "Intercept"                             
## [2] "Conditions_T24_NPS_AZD_vs_T24_NPS_DMSO"
## [3] "Conditions_T24_NS_DMSO_vs_T24_NPS_DMSO"
## [4] "Conditions_T24_NS_AZD_vs_T24_NPS_DMSO" 
## [5] "Conditions_T24_NP_DMSO_vs_T24_NPS_DMSO"
## [6] "Conditions_T24_NP_AZD_vs_T24_NPS_DMSO"

7.4.1 Nutrition effect of carbon starvation

7.4.1.1 Extraction of the results from the DESeq analysis

res <- results(dds,name = "Conditions_T24_NP_DMSO_vs_T24_NPS_DMSO")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T24_NP_DMSO_vs_T24_NPS_DMSO.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
SucEffect24hrs <- rownames(res[cutoffs,])
SucLow24hrs <- rownames(res[cutoff2,])
SucHigh24hrs <- rownames(res[cutoff1,])

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 2286 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 1190 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 1096 genes that are repressed

7.4.1.2 MA plot

DESeq2::plotMA(res)

7.4.1.3 Volcano plot

volcanoPlot(res, lfc=1)

7.4.1.4 Heatmap

hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
                Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
                distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
                hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))

7.4.2 Nutrition effect of phosphorus starvation

7.4.2.1 Extraction of the results from the DESeq analysis

res <- results(dds,name = "Conditions_T24_NS_DMSO_vs_T24_NPS_DMSO")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T24_NS_DMSO_vs_T24_NPS_DMSO.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
PiEffect24hrs <- rownames(res[cutoffs,])
PiLow24hrs <- rownames(res[cutoff2,])
PiHigh24hrs <- rownames(res[cutoff1,])

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 7958 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 4057 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 3901 genes that are repressed

7.4.2.2 MA plot

DESeq2::plotMA(res)

7.4.2.3 Volcano plot

volcanoPlot(res, lfc = 1)

7.4.2.4 Heatmap

hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
                Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
                distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
                hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))

7.4.3 Effect of AZD-8055

7.4.3.1 Extraction of the results from the DESeq analysis

res <- results(dds,name = "Conditions_T24_NPS_AZD_vs_T24_NPS_DMSO")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T24_NPS_AZD_vs_T24_NPS_DMSO.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
AzdEffect24hrs <- rownames(res[cutoffs,])
AzdLow24hrs <- rownames(res[cutoff2,])
AzdHigh24hrs <- rownames(res[cutoff1,])

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 9852 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 4857 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 4995 genes that are repressed

7.4.3.2 MA plot

DESeq2::plotMA(res)

7.4.3.3 Volcano plot

volcanoPlot(res, lfc=1)

7.4.3.4 Heatmap

hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
                Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
                distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
                hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))

7.4.4 Combined effect of AZD treatment and sugar starvation

7.4.4.1 Extraction of the results from the DESeq analysis

res <- results(dds,name = "Conditions_T24_NP_AZD_vs_T24_NPS_DMSO")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T24_NP_AZD_vs_T24_NPS_DMSO.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
AzdNP24hrs <- rownames(res[cutoffs,])
AzdNPLow24hrs <- rownames(res[cutoff2,])
AzdNPHigh24hrs <- rownames(res[cutoff1,])

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 11535 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 5956 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 5579 genes that are repressed

7.4.4.2 MA plot

DESeq2::plotMA(res)

7.4.4.3 Volcano plot

volcanoPlot(res, lfc=1)

7.4.4.4 Heatmap

hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
                Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
                distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
                hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))

7.4.5 Combined effect of AZD treatment and phosphorus starvation

7.4.5.1 Extraction of the results from the DESeq analysis

res <- results(dds,name = "Conditions_T24_NS_AZD_vs_T24_NPS_DMSO")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T24_NS_AZD_vs_T24_NPS_DMSO.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
AzdNS24hrs <- rownames(res[cutoffs,])
AzdNSLow24hrs <- rownames(res[cutoff2,])
AzdNSHigh24hrs <- rownames(res[cutoff1,])

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 10805 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 5446 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 5359 genes that are repressed

7.4.5.2 MA plot

DESeq2::plotMA(res)

7.4.5.3 Volcano plot

volcanoPlot(res, lfc=1)

7.4.5.4 Heatmap

hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
                Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
                distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
                hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))

8 Export list of DEGs

write.table(AzdHigh24hrs, file = "AzdHigh24hrs.csv", sep=";", row.names = FALSE)
write.table(AzdHigh6hrs, file = "AzdHigh6hrs.csv", sep=";", row.names = FALSE)
write.table(PiHigh24hrs, file = "PiHigh24hrs.csv", sep=";", row.names = FALSE)
write.table(PiHigh6hrs, file = "PiHigh6hrs.csv", sep=";", row.names = FALSE)
write.table(SucHigh24hrs, file = "SucHigh24hrs.csv", sep=";", row.names = FALSE)
write.table(SucHigh6hrs, file = "SucHigh6hrs.csv", sep=";", row.names = FALSE)

write.table(AzdLow24hrs, file = "AzdLow24hrs.csv", sep=";", row.names = FALSE)
write.table(AzdLow6hrs, file = "AzdLow6hrs.csv", sep=";", row.names = FALSE)
write.table(PiLow24hrs, file = "PiLow24hrs.csv", sep=";", row.names = FALSE)
write.table(PiLow6hrs, file = "PiLow6hrs.csv", sep=";", row.names = FALSE)
write.table(SucLow24hrs, file = "SucLow24hrs.csv", sep=";", row.names = FALSE)
write.table(SucLow6hrs, file = "SucLow6hrs.csv", sep=";", row.names = FALSE)

write.table(AzdNPLow6hrs, file = "AzdNPLow6hrs.csv", sep=";", row.names = FALSE)
write.table(AzdNPHigh6hrs, file = "AzdNPHigh6hrs.csv", sep=";", row.names = FALSE)
write.table(AzdNPLow24hrs, file = "AzdNPLow24hrs.csv", sep=";", row.names = FALSE)
write.table(AzdNPHigh24hrs, file = "AzdNPHigh24hrs.csv", sep=";", row.names = FALSE)

write.table(AzdNSLow6hrs, file = "AzdNSLow6hrs.csv", sep=";", row.names = FALSE)
write.table(AzdNSHigh6hrs, file = "AzdNSHigh6hrs.csv", sep=";", row.names = FALSE)
write.table(AzdNSLow24hrs, file = "AzdNSLow24hrs.csv", sep=";", row.names = FALSE)
write.table(AzdNSHigh24hrs, file = "AzdNSHigh24hrs.csv", sep=";", row.names = FALSE)

9 Comparisons of GOI lists (Venn diagrams)

9.1 Nutrition re-supply effect

plot.new()
grid.draw(venn.diagram(list(NPS_DMSO_High_6hrs, NPS_DMSO_High_24hrs),
                       filename=NULL,
                       col=c("yellow","orange"),
                       category.names=c("T6_up","T24_up")))

plot.new()
grid.draw(venn.diagram(list(NPS_DMSO_Low_6hrs, NPS_DMSO_Low_24hrs),
                       filename=NULL,
                       col=c("turquoise","blue"),
                       category.names=c("T6_up","T24_up")))

9.2 GOI at T6

9.2.1 Comparison of AZD treatment with starvations

  • Downregulated genes
plot.new()
grid.draw(venn.diagram(list(AzdLow6hrs, PiLow6hrs, SucLow6hrs),
                       filename=NULL,
                       col=pal[1:3],
                       category.names=c("AZD","Phos. Starv.","Suc. Starv.")))

  • Upregulated genes
plot.new()
grid.draw(venn.diagram(list(AzdHigh6hrs, PiHigh6hrs, SucHigh6hrs),
                       filename=NULL,
                       col=pal[1:3],
                       category.names=c("AZD","Phos. Starv.","Suc. Starv.")))

9.3 GOI at T24

#’ ### Comparison of AZD treatment with starvations * Downregulated genes

plot.new()
grid.draw(venn.diagram(list(AzdLow24hrs, PiLow24hrs, SucLow24hrs),
                       filename=NULL,
                       col=pal[1:3],
                       category.names=c("AZD","Phos. Starv.","Suc. Starv.")))

  • Upregulated genes
plot.new()
grid.draw(venn.diagram(list(AzdHigh24hrs, PiHigh24hrs, SucHigh24hrs),
                       filename=NULL,
                       col=pal[1:3],
                       category.names=c("AZD","Phos. Starv.","Suc. Starv.")))

10 GO enrichment analysis

10.1 For AZD treatment

  • Induced genes after 6hrs
GO <- gopher(AzdHigh6hrs,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana", alpha=2)
## Loading required package: jsonlite
## 
## Attaching package: 'jsonlite'
## The following object is masked from 'package:purrr':
## 
##     flatten
## No enrichments found in task: mapman
write.table(GO$go, file = "GO_AzdHigh6hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$kegg, file = "KEGG_AzdHigh6hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$pfam, file = "PFAM_AzdHigh6hrs.csv", sep = ";", row.names = FALSE)
  • Induced genes after 24hrs
GO <- gopher(AzdHigh24hrs,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana",alpha=2)
## No enrichments found in task: mapman
write.table(GO$go, file = "GO_AzdHigh24hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$kegg, file = "KEGG_AzdHigh24hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$pfam, file = "PFAM_AzdHigh24hrs.csv", sep = ";", row.names = FALSE)
  • Repressed genes after 6hrs
GO <- gopher(AzdLow6hrs,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana",alpha=2)
## No enrichments found in task: mapman
write.table(GO$go, file = "GO_AzdLow6hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$kegg, file = "KEGG_AzdLow6hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$pfam, file = "PFAM_AzdLow6hrs.csv", sep = ";", row.names = FALSE)
  • Repressed genes after 24hrs
GO <- gopher(AzdLow24hrs,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana",alpha=2)
## No enrichments found in task: mapman
write.table(GO$go, file = "GO_AzdLow24hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$kegg, file = "KEGG_AzdLow24hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$pfam, file = "PFAM_AzdLow24hrs.csv", sep = ";", row.names = FALSE)

10.2 For Sucrose starvation

  • Induced genes after 6hrs
GO <- gopher(SucHigh6hrs,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana", alpha=2)
## No enrichments found in task: mapman
write.table(GO$go, file = "GO_SucHigh6hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$kegg, file = "KEGG_SucHigh6hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$pfam, file = "PFAM_SucHigh6hrs.csv", sep = ";", row.names = FALSE)
  • Induced genes after 24hrs
GO <- gopher(SucHigh24hrs,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana", alpha=2)
## No enrichments found in task: mapman
write.table(GO$go, file = "GO_SucHigh24hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$kegg, file = "KEGG_SucHigh24hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$pfam, file = "PFAM_SucHigh24hrs.csv", sep = ";", row.names = FALSE)
  • Repressed genes after 6hrs
GO <- gopher(SucLow6hrs,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana", alpha=2)
## No enrichments found in task: mapman
write.table(GO$go, file = "GO_SucLow6hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$kegg, file = "KEGG_SucLow6hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$pfam, file = "PFAM_SucLow6hrs.csv", sep = ";", row.names = FALSE)
  • Repressed genes after 24hrs
GO <- gopher(SucLow24hrs,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana", alpha=2)
## No enrichments found in task: mapman
write.table(GO$go, file = "GO_SucLow24hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$kegg, file = "KEGG_SucLow24hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$pfam, file = "PFAM_SucLow24hrs.csv", sep = ";", row.names = FALSE)

10.3 For Phosphorus starvation

  • Induced genes after 6hrs
GO <- gopher(PiHigh6hrs,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana", alpha=2)
## No enrichments found in task: mapman
write.table(GO$go, file = "GO_PiHigh6hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$kegg, file = "KEGG_PiHigh6hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$pfam, file = "PFAM_PiHigh6hrs.csv", sep = ";", row.names = FALSE)
  • Induced genes after 24hrs
GO <- gopher(PiHigh24hrs,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana", alpha=2)
## No enrichments found in task: mapman
write.table(GO$go, file = "GO_PiHigh24hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$kegg, file = "KEGG_PiHigh24hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$pfam, file = "PFAM_PiHigh24hrs.csv", sep = ";", row.names = FALSE)
  • Repressed genes after 6hrs
GO <- gopher(PiLow6hrs,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana", alpha=2)
## No enrichments found in task: mapman
write.table(GO$go, file = "GO_PiLow6hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$kegg, file = "KEGG_PiLow6hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$pfam, file = "PFAM_PiLow6hrs.csv", sep = ";", row.names = FALSE)
  • Repressed genes after 24hrs
GO <- gopher(PiLow24hrs,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana", alpha=2)
## No enrichments found in task: mapman
write.table(GO$go, file = "GO_PiLow24hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$kegg, file = "KEGG_PiLow24hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$pfam, file = "PFAM_PiLow24hrs.csv", sep = ";", row.names = FALSE)

10.4 For the interaction between AZD treatment and phosphorus starvation

  • Induced genes after 6hrs
GO <- gopher(AzdNSHigh6hrs,background=rownames(vsd),url="athaliana", alpha=2)
## No enrichments found in task: mapman
write.table(GO$go, file = "GO_AzdNSHigh6hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$kegg, file = "KEGG_AzdNSHigh6hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$pfam, file = "PFAM_AzdNSHigh6hrs.csv", sep = ";", row.names = FALSE)
  • Induced genes after 24hrs
GO <- gopher(AzdNSHigh24hrs,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana", alpha=2)
## No enrichments found in task: mapman
write.table(GO$go, file = "GO_AzdNSHigh24hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$kegg, file = "KEGG_AzdNSHigh24hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$pfam, file = "PFAM_AzdNSHigh24hrs.csv", sep = ";", row.names = FALSE)
  • Repressed genes after 6hrs
GO <- gopher(AzdNSLow6hrs,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana", alpha=2)
## No enrichments found in task: mapman
write.table(GO$go, file = "GO_AzdNSLow6hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$kegg, file = "KEGG_AzdNSLow6hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$pfam, file = "PFAM_AzdNSLow6hrs.csv", sep = ";", row.names = FALSE)
  • Repressed genes after 24hrs
GO <- gopher(AzdNSLow24hrs,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana", alpha=2)
## No enrichments found in task: mapman
write.table(GO$go, file = "GO_AzdNSLow24hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$kegg, file = "KEGG_AzdNSLow24hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$pfam, file = "PFAM_AzdNSLow24hrs.csv", sep = ";", row.names = FALSE)

10.5 For the interaction between AZD treatment and sugar starvation

  • Induced genes after 6hrs
GO <- gopher(AzdNPHigh6hrs,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana", alpha=2)
## No enrichments found in task: mapman
write.table(GO$go, file = "GO_AzdNPHigh6hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$kegg, file = "KEGG_AzdNPHigh6hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$pfam, file = "PFAM_AzdNPHigh6hrs.csv", sep = ";", row.names = FALSE)
  • Induced genes after 24hrs
GO <- gopher(AzdNPHigh24hrs,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana", alpha=2)
## No enrichments found in task: mapman
write.table(GO$go, file = "GO_AzdNPHigh24hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$kegg, file = "KEGG_AzdNPHigh24hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$pfam, file = "PFAM_AzdNPHigh24hrs.csv", sep = ";", row.names = FALSE)
  • Repressed genes after 6hrs
GO <- gopher(AzdNPLow6hrs,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana", alpha=2)
## No enrichments found in task: mapman
write.table(GO$go, file = "GO_AzdNPLow6hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$kegg, file = "KEGG_AzdNPLow6hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$pfam, file = "PFAM_AzdNPLow6hrs.csv", sep = ";", row.names = FALSE)
  • Repressed genes after 24hrs
GO <- gopher(AzdNPLow24hrs,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana", alpha=2)
## No enrichments found in task: mapman
write.table(GO$go, file = "GO_AzdNPLow24hrs.csv", sep = ";", row.names = FALSE)
write.table(GO$kegg, file = "KEGG_AzdNPLow24hrs.csv", sep = ";", row.names = FALSE) 
write.table(GO$pfam, file = "PFAM_AzdNPLow24hrs.csv", sep = ";", row.names = FALSE)

11 Expression level analysis of specific gene lists

levels(samples$Conditions)
##  [1] "T24_NPS_DMSO" "T6_NPS_DMSO"  "T0_T0_0"      "T6_NPS_AZD"   "T6_NS_DMSO"  
##  [6] "T6_NS_AZD"    "T6_NP_DMSO"   "T6_NP_AZD"    "T24_NPS_AZD"  "T24_NS_DMSO" 
## [11] "T24_NS_AZD"   "T24_NP_DMSO"  "T24_NP_AZD"
sel_T0 <- samples$Timepoint %in% c("T0","T6","T24")

suppressMessages(dds_T0 <- DESeqDataSetFromMatrix(
  countData = kg[,sel_T0],
  colData = samples[sel_T0,],
  design = ~ Conditions))

11.1 Differential expression analysis

dds_T0 <- DESeq(dds_T0)
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 2 genes
## -- DESeq argument 'minReplicatesForReplace' = 7 
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing

11.2 Variance Stabilising Transformation

11.2.1 Perform a Variance Stabilizing Transformation for plotting

vst_T0 <- varianceStabilizingTransformation(dds_T0,blind=FALSE)
vsd_T0 <- assay(vst_T0)
vsd_T0 <- vsd_T0 - min(vsd_T0)

11.3 Export the complete list of averages and SDs

sel1 <- rownames(vsd_T0)
expr <- vsd_T0[match(sel1,rownames(vsd_T0)),]
Avg <- sapply(split.data.frame(t(expr),
                               f = droplevels(samples$Conditions[sel_T0])),
              colMeans)
SD <- sapply(split.data.frame(t(expr),f = droplevels(samples$Conditions[sel_T0])),colSds)
rownames(SD) <- rownames(Avg)
write.table(Avg, file = "Averaged_Normalized_Counts.csv", sep = ";", row.names = FALSE, dec=",")
write.table(rownames(Avg), file = "Averaged_Normalized_Counts_genes.csv", sep = ";", row.names = FALSE, dec=",")

11.4 TOR complex members

11.4.1 Preparation of the complex member list

sel1 <- c("AT1G50030","AT3G18140","AT2G22040","AT3G08850","AT5G01770") 

11.4.2 Preparation of the expression table for the shortlisted genes

AvgTOR <- Avg[match(sel1,rownames(Avg)),]
SDTOR <- SD[match(sel1,rownames(SD)),]

11.4.3 Graphical representations

11.4.3.1 Combined barplots

AvgTOR2 <- t(AvgTOR)
SDTOR2 <- t(SDTOR)
barcenters <- barplot(AvgTOR2,beside=T, cex.names=0.7,legend.text = rownames(AvgTOR2),ylim=c(0,4))
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR2-SDTOR2, y1=AvgTOR2+SDTOR2,
       lwd=1.5, angle=90, length=0.05,code=3)
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR2 - SDTOR2, :
## zero-length arrow is of indeterminate angle and so skipped

11.4.3.2 Separated barplots

for (i in 1:length(AvgTOR[,1])){
  barcenters <- barplot(AvgTOR[i,],beside=T, cex.names=0.7,legend.text = sel1[i],ylim=c(0,4))
  arrows(x0=barcenters, x1=barcenters, y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
         lwd=1.5, angle=90, length=0.2,code=3)
}

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

11.4.3.3 Individual graphs without colors

for (i in 1:length(AvgTOR[,1]))
{
  plot(AvgTOR[i,],ylim=c(min(AvgTOR[i,]-SDTOR[i,]),max(AvgTOR[i,]+SDTOR[i,])),
       xaxt="n",xlab="",ylab=sprintf("gene = %s",rownames(AvgTOR)[i]))
  axis(side = 1,at=1:13, colnames(AvgTOR),cex.axis=0.7,las=2)
  arrows(x0=1:length(AvgTOR[i,]), x1=1:length(AvgTOR[i,]),
         y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
         lwd=1.5, angle=90, length=0.05,code=3)
}

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

11.4.3.4 Individual graphs with colors

a <- matrix(NA, nrow=6, ncol=3)
colnames(a) <- c(0,6,24)
rownames(a) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
b <- matrix(NA, nrow=6, ncol=3)
colnames(b) <- c(0,6,24)
rownames(b) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")


for (i in 1:length(AvgTOR[,1]))
{
  a[1:6,1] <- AvgTOR[i,1]
  a[1:6,2] <- AvgTOR[i,2:7]
  a[1:6,3] <- AvgTOR[i,8:13]
  
  b[1:6,1] <- SDTOR[i,1]
  b[1:6,2] <- SDTOR[i,2:7]
  b[1:6,3] <- SDTOR[i,8:13]
  
  plot(colnames(a),a[1,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),ylab=rownames(AvgTOR)[i])
  lines(colnames(a),a[2,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),lty=2)
  lines(colnames(a),a[3,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise")
  lines(colnames(a),a[4,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise",lty=2)
  lines(colnames(a),a[5,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3")
  lines(colnames(a),a[6,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3",lty=2)
  
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[1,] - b[1,],
         y1=a[1,] + b[1,],
         lwd=1, angle=90, length=0.05, code=3)
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[2,] - b[2,],
         y1=a[2,] + b[2,],
         lwd=1, angle=90, length=0.05, code=3)
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[3,] - b[3,],
         y1=a[3,] + b[3,],
         lwd=1, angle=90, length=0.05, code=3, col="turquoise")
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[4,] - b[4,],
         y1=a[4,] + b[4,],
         lwd=1, angle=90, length=0.05, code=3, col="turquoise")
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[5,] - b[5,],
         y1=a[5,] + b[5,],
         lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[6,] - b[6,],
         y1=a[6,] + b[6,],
         lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
}

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

11.4.3.5 Heatmap

AvgTOR[AvgTOR == 0] <- 0.000001
AvgTOR_norm <- log2(AvgTOR[,] / AvgTOR[,1])
AvgTOR_norm[AvgTOR_norm < -0.5] <- -0.5; AvgTOR_norm[AvgTOR_norm > 0.5] <- 0.5


heatmap.2(AvgTOR_norm,
          col=hpal,
          dendrogram="none",
          trace="none",
          Colv=FALSE,
          Rowv=FALSE,
          margins=c(8,12))

11.4.4 Graphical representations of all the samples

11.4.4.1 Preparation of the sample data

sel1 <- c("AT1G50030","AT3G18140","AT3G08850","AT5G01770")
AvgTOR <- Avg[match(sel1,rownames(Avg)),]
TOR <- vsd_T0[match(sel1,rownames(vsd_T0)),]
TOR_norm <- TOR/AvgTOR[,1]
TOR_norm <- log2(TOR_norm)
colnames(TOR_norm) <- samples$Conditions


a <- match(colnames(TOR_norm),samples$Conditions)
plot(TOR_norm[4,] ~ a, ylim=c(-0.5,0.5),main="AT5G01770")
b <- c(1,9,12,21,24,15,18,27,30,39,42,33,36)
lines(b,AvgTOR_norm[5,])

11.5 Genes involved in the cell cycle

11.5.1 Preparation of a list of genes of the cell cycle

sel1 <- read.csv("~/arabidopsis-nutrition-TOR/seidr/cell_cycle_genes.csv", sep=";")[,1]

11.6 Preparation of the expression table for the shortlisted genes

AvgTOR <- Avg[match(sel1,rownames(Avg)),]
SDTOR <- SD[match(sel1,rownames(SD)),]

11.6.1 Graphical representations

11.6.1.1 Combined barplots

barcenters <- barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = sel1,ylim=c(0,4))
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR-SDTOR, y1=AvgTOR+SDTOR,
       lwd=1.5, angle=90, length=0.05,code=3)
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

11.6.1.2 Individual graphs without colors

for (i in 1:length(AvgTOR[,1]))
{
  plot(AvgTOR[i,],ylim=c(min(AvgTOR[i,]-SDTOR[i,]),max(AvgTOR[i,]+SDTOR[i,])),
       xaxt="n",xlab="",ylab=sprintf("gene = %s",rownames(AvgTOR)[i]))
  axis(side = 1,at=1:13, colnames(AvgTOR),cex.axis=0.7,las=2)
  arrows(x0=1:length(AvgTOR[i,]), x1=1:length(AvgTOR[i,]),
         y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
         lwd=1.5, angle=90, length=0.05,code=3)
}

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

11.6.1.3 Individual graphs with colors

a <- matrix(NA, nrow=6, ncol=3)
colnames(a) <- c(0,6,24)
rownames(a) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
b <- matrix(NA, nrow=6, ncol=3)
colnames(b) <- c(0,6,24)
rownames(b) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")


for (i in 1:length(AvgTOR[,1]))
{
  a[1:6,1] <- AvgTOR[i,1]
  a[1:6,2] <- AvgTOR[i,2:7]
  a[1:6,3] <- AvgTOR[i,8:13]
  
  b[1:6,1] <- SDTOR[i,1]
  b[1:6,2] <- SDTOR[i,2:7]
  b[1:6,3] <- SDTOR[i,8:13]
  
  plot(colnames(a),a[1,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),ylab=rownames(AvgTOR)[i])
  lines(colnames(a),a[2,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),lty=2)
  lines(colnames(a),a[3,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise")
  lines(colnames(a),a[4,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise",lty=2)
  lines(colnames(a),a[5,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3")
  lines(colnames(a),a[6,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3",lty=2)
  
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[1,] - b[1,],
         y1=a[1,] + b[1,],
         lwd=1, angle=90, length=0.05, code=3)
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[2,] - b[2,],
         y1=a[2,] + b[2,],
         lwd=1, angle=90, length=0.05, code=3)
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[3,] - b[3,],
         y1=a[3,] + b[3,],
         lwd=1, angle=90, length=0.05, code=3, col="turquoise")
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[4,] - b[4,],
         y1=a[4,] + b[4,],
         lwd=1, angle=90, length=0.05, code=3, col="turquoise")
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[5,] - b[5,],
         y1=a[5,] + b[5,],
         lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[6,] - b[6,],
         y1=a[6,] + b[6,],
         lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
}

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

11.6.1.4 Heatmap

AvgTOR[AvgTOR == 0] <- 0.000001
AvgTOR_norm <- log2(AvgTOR[,] / AvgTOR[,1])

AvgTOR_norm[AvgTOR_norm < -3] <- -3; AvgTOR_norm[AvgTOR_norm > 3] <- 3

heatmap.2(AvgTOR_norm,
          col=hpal,
          dendrogram="none",
          trace="none",
          Colv=FALSE,
          Rowv=FALSE,
          margins=c(8,8),
          labRow = read.csv("~/arabidopsis-nutrition-TOR/seidr/cell_cycle_genes.csv", sep=";")[,2])

heatmap.2(AvgTOR_norm,
          trace="none",
          col=hpal,
          Colv=FALSE,
          dendrogram = "row",
          labRow = read.csv("~/arabidopsis-nutrition-TOR/seidr/cell_cycle_genes.csv", sep=";")[,2],
          margins=c(8,8),
          hclustfun = function(X){hclust(X,method="ward.D2")})

11.7 Histone genes

11.7.1 List of Histone H3 family members excluding the “AT1G75610” which was not detected and the “AT1G19890” which was found detected only in the T0 sample

sel1 <- c("AT5G65360","AT1G09200","AT3G27360","AT5G10400","AT5G65350","AT5G10390","AT4G40030",
          "AT4G40040","AT5G10980","AT1G13370","AT1G75600","AT1G01370") 

11.7.2 Preparation of the expression table for the shortlisted genes

AvgTOR <- Avg[match(sel1,rownames(Avg)),]
SDTOR <- SD[match(sel1,rownames(SD)),]

11.7.3 Graphical representations

11.7.3.1 Combined barplots

barcenters <- barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = sel1)
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR-SDTOR, y1=AvgTOR+SDTOR,
       lwd=1.5, angle=90, length=0.05,code=3)

11.7.3.2 Separated barplots

for (i in 1:length(AvgTOR[,1])){
  barcenters <- barplot(AvgTOR[i,],beside=T, cex.names=0.7,legend.text = sel1[i], las=2)
  arrows(x0=barcenters, x1=barcenters, y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
         lwd=1.5, angle=90, length=0.2,code=3)
}

11.7.3.3 Individual graphs without colors

for (i in 1:length(AvgTOR[,1]))
{
  plot(AvgTOR[i,],ylim=c(min(AvgTOR[i,]-SDTOR[i,]),max(AvgTOR[i,]+SDTOR[i,])),
       xaxt="n",xlab="",ylab=sprintf("gene = %s",rownames(AvgTOR)[i]))
  axis(side = 1,at=1:13, colnames(AvgTOR),cex.axis=0.7,las=2)
  arrows(x0=1:length(AvgTOR[i,]), x1=1:length(AvgTOR[i,]),
         y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
         lwd=1.5, angle=90, length=0.05,code=3)
}

11.7.3.4 Individual graphs with colors

a <- matrix(NA, nrow=6, ncol=3)
colnames(a) <- c(0,6,24)
rownames(a) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
b <- matrix(NA, nrow=6, ncol=3)
colnames(b) <- c(0,6,24)
rownames(b) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")


for (i in 1:length(AvgTOR[,1]))
{
  a[1:6,1] <- AvgTOR[i,1]
  a[1:6,2] <- AvgTOR[i,2:7]
  a[1:6,3] <- AvgTOR[i,8:13]
  
  b[1:6,1] <- SDTOR[i,1]
  b[1:6,2] <- SDTOR[i,2:7]
  b[1:6,3] <- SDTOR[i,8:13]
  
  plot(colnames(a),a[1,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),ylab=rownames(AvgTOR)[i])
  lines(colnames(a),a[2,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),lty=2)
  lines(colnames(a),a[3,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise")
  lines(colnames(a),a[4,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise",lty=2)
  lines(colnames(a),a[5,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3")
  lines(colnames(a),a[6,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3",lty=2)
  
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[1,] - b[1,],
         y1=a[1,] + b[1,],
         lwd=1, angle=90, length=0.05, code=3)
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[2,] - b[2,],
         y1=a[2,] + b[2,],
         lwd=1, angle=90, length=0.05, code=3)
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[3,] - b[3,],
         y1=a[3,] + b[3,],
         lwd=1, angle=90, length=0.05, code=3, col="turquoise")
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[4,] - b[4,],
         y1=a[4,] + b[4,],
         lwd=1, angle=90, length=0.05, code=3, col="turquoise")
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[5,] - b[5,],
         y1=a[5,] + b[5,],
         lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[6,] - b[6,],
         y1=a[6,] + b[6,],
         lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
}

11.7.3.5 Heatmap

AvgTOR[AvgTOR == 0] <- 0.000001
AvgTOR_norm <- log2(AvgTOR[,] / AvgTOR[,1])
AvgTOR_norm[AvgTOR_norm < -3] <- -3; AvgTOR_norm[AvgTOR_norm > 3] <- 3


heatmap.2(AvgTOR_norm,
          col=hpal,
          dendrogram="none",
          trace="none",
          Colv=FALSE,
          Rowv=FALSE,
          margins=c(8,12))

11.8 Genes involved in the response to phosphate starvation

11.8.1 Preparation of the transporter list (Poirier and Bucher, 2002) and phosphatases (Hanchi, PhD thesis) and Pi starvation responsive genes (Wang et al., 2018, Front. Plant Sci.)

sel1 <- c("AT5G43350","AT5G43370","AT5G43360","AT2G38940","AT2G32830","AT5G43340","AT3G54700",
          "AT1G20860","AT1G76430","AT3G26570","AT5G14040","AT3G48850","AT2G17270","AT5G46110",
          "AT5G33320","AT5G54800","AT1G61800","AT5G17640","AT1G73010","AT1G17710",
          "AT3G09922" ,"AT2G02990","AT3G17790") 

sel1 <- c("AT5G43350","AT5G43370","AT5G43360","AT2G38940","AT2G32830","AT5G43340","AT3G54700",
          "AT1G20860","AT1G76430","AT3G26570","AT5G14040","AT3G48850","AT2G17270","AT5G46110",
          "AT5G33320","AT5G54800","AT1G61800","AT5G17640","AT1G73010","AT1G17710") 

11.8.2 Preparation of the expression table for the shortlisted genes

AvgTOR <- Avg[match(sel1,rownames(Avg)),]
SDTOR <- SD[match(sel1,rownames(SD)),]

11.8.3 Graphical representations

11.8.3.1 Combined barplots

barcenters <- barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = sel1)
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR-SDTOR, y1=AvgTOR+SDTOR,
       lwd=1.5, angle=90, length=0.05,code=3)
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

11.8.3.2 Separated barplots

for (i in 1:length(AvgTOR[,1])){
  barcenters <- barplot(AvgTOR[i,],beside=T, cex.names=0.7,legend.text = sel1[i], las=2)
  arrows(x0=barcenters, x1=barcenters, y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
         lwd=1.5, angle=90, length=0.2,code=3)
}

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

11.8.3.3 Individual graphs without colors

for (i in 1:length(AvgTOR[,1]))
{
  plot(AvgTOR[i,],ylim=c(min(AvgTOR[i,]-SDTOR[i,]),max(AvgTOR[i,]+SDTOR[i,])),
       xaxt="n",xlab="",ylab=sprintf("gene = %s",rownames(AvgTOR)[i]))
  axis(side = 1,at=1:13, colnames(AvgTOR),cex.axis=0.7,las=2)
  arrows(x0=1:length(AvgTOR[i,]), x1=1:length(AvgTOR[i,]),
         y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
         lwd=1.5, angle=90, length=0.05,code=3)
}

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

11.8.3.4 Individual graphs with colors

a <- matrix(NA, nrow=6, ncol=3)
colnames(a) <- c(0,6,24)
rownames(a) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
b <- matrix(NA, nrow=6, ncol=3)
colnames(b) <- c(0,6,24)
rownames(b) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")


for (i in 1:length(AvgTOR[,1]))
{
  a[1:6,1] <- AvgTOR[i,1]
  a[1:6,2] <- AvgTOR[i,2:7]
  a[1:6,3] <- AvgTOR[i,8:13]
  
  b[1:6,1] <- SDTOR[i,1]
  b[1:6,2] <- SDTOR[i,2:7]
  b[1:6,3] <- SDTOR[i,8:13]
  
  plot(colnames(a),a[1,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),ylab=rownames(AvgTOR)[i])
  lines(colnames(a),a[2,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),lty=2)
  lines(colnames(a),a[3,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise")
  lines(colnames(a),a[4,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise",lty=2)
  lines(colnames(a),a[5,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3")
  lines(colnames(a),a[6,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3",lty=2)
  
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[1,] - b[1,],
         y1=a[1,] + b[1,],
         lwd=1, angle=90, length=0.05, code=3)
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[2,] - b[2,],
         y1=a[2,] + b[2,],
         lwd=1, angle=90, length=0.05, code=3)
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[3,] - b[3,],
         y1=a[3,] + b[3,],
         lwd=1, angle=90, length=0.05, code=3, col="turquoise")
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[4,] - b[4,],
         y1=a[4,] + b[4,],
         lwd=1, angle=90, length=0.05, code=3, col="turquoise")
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[5,] - b[5,],
         y1=a[5,] + b[5,],
         lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[6,] - b[6,],
         y1=a[6,] + b[6,],
         lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
}

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

11.8.3.5 Heatmap

AvgTOR[AvgTOR == 0] <- 0.000001
AvgTOR_norm <- log2(AvgTOR[,] / AvgTOR[,1])
AvgTOR_norm[AvgTOR_norm < -3] <- -3; AvgTOR_norm[AvgTOR_norm > 3] <- 3


heatmap.2(AvgTOR_norm,
          col=hpal,
          dendrogram="none",
          trace="none",
          Colv=FALSE,
          Rowv=FALSE,
          margins=c(8,12))

11.8.4 Preparation of the systemically-regulated genes by Pi starvation (Thibaud et al., 2010)

sel1 <- c('AT5G01220','AT3G02870','AT3G17790','AT5G64000','AT3G52820','AT2G11810','AT1G73010',
          'AT3G03540','AT3G02040','AT5G20410','AT3G05630','AT4G33030','AT2G27190','AT4G00550',
          'AT2G45130','AT5G20150','AT2G26660','AT1G68740','AT2G32830','AT2G38940','AT1G20860',
          'AT3G58810','AT5G56080','AT5G04950','AT1G23020','AT4G19690','AT3G46900','AT4G19680',
          'AT1G09790','AT3G58060','AT5G03570','AT2G28160','AT2G03260','AT1G74770','AT4G09110',
          'AT5G06490','AT1G49390','AT1G72200','AT2G35000','AT3G12900','AT4G30120') 

11.8.5 Preparation of the expression table for the shortlisted genes

AvgTOR <- Avg[match(sel1,rownames(Avg)),]
SDTOR <- SD[match(sel1,rownames(SD)),]

11.8.6 Graphical representations

11.8.6.1 Combined barplots

barcenters <- barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = sel1)
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR-SDTOR, y1=AvgTOR+SDTOR,
       lwd=1.5, angle=90, length=0.05,code=3)
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

11.8.6.2 Separated barplots

for (i in 1:length(AvgTOR[,1])){
  barcenters <- barplot(AvgTOR[i,],beside=T, cex.names=0.7,legend.text = sel1[i], las=2)
  arrows(x0=barcenters, x1=barcenters, y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
         lwd=1.5, angle=90, length=0.2,code=3)
}

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

11.8.6.3 Individual graphs without colors

for (i in 1:length(AvgTOR[,1]))
{
  plot(AvgTOR[i,],ylim=c(min(AvgTOR[i,]-SDTOR[i,]),max(AvgTOR[i,]+SDTOR[i,])),
       xaxt="n",xlab="",ylab=sprintf("gene = %s",rownames(AvgTOR)[i]))
  axis(side = 1,at=1:13, colnames(AvgTOR),cex.axis=0.7,las=2)
  arrows(x0=1:length(AvgTOR[i,]), x1=1:length(AvgTOR[i,]),
         y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
         lwd=1.5, angle=90, length=0.05,code=3)
}

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

11.8.6.4 Individual graphs with colors

a <- matrix(NA, nrow=6, ncol=3)
colnames(a) <- c(0,6,24)
rownames(a) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
b <- matrix(NA, nrow=6, ncol=3)
colnames(b) <- c(0,6,24)
rownames(b) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")


for (i in 1:length(AvgTOR[,1]))
{
  a[1:6,1] <- AvgTOR[i,1]
  a[1:6,2] <- AvgTOR[i,2:7]
  a[1:6,3] <- AvgTOR[i,8:13]
  
  b[1:6,1] <- SDTOR[i,1]
  b[1:6,2] <- SDTOR[i,2:7]
  b[1:6,3] <- SDTOR[i,8:13]
  
  plot(colnames(a),a[1,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),ylab=rownames(AvgTOR)[i])
  lines(colnames(a),a[2,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),lty=2)
  lines(colnames(a),a[3,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise")
  lines(colnames(a),a[4,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise",lty=2)
  lines(colnames(a),a[5,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3")
  lines(colnames(a),a[6,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3",lty=2)
  
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[1,] - b[1,],
         y1=a[1,] + b[1,],
         lwd=1, angle=90, length=0.05, code=3)
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[2,] - b[2,],
         y1=a[2,] + b[2,],
         lwd=1, angle=90, length=0.05, code=3)
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[3,] - b[3,],
         y1=a[3,] + b[3,],
         lwd=1, angle=90, length=0.05, code=3, col="turquoise")
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[4,] - b[4,],
         y1=a[4,] + b[4,],
         lwd=1, angle=90, length=0.05, code=3, col="turquoise")
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[5,] - b[5,],
         y1=a[5,] + b[5,],
         lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[6,] - b[6,],
         y1=a[6,] + b[6,],
         lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
}

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

11.8.6.5 Heatmap

AvgTOR[AvgTOR == 0] <- 0.000001
AvgTOR_norm <- log2(AvgTOR[,] / AvgTOR[,1])
AvgTOR_norm[AvgTOR_norm < -3] <- -3; AvgTOR_norm[AvgTOR_norm > 3] <- 3


heatmap.2(AvgTOR_norm,
          col=hpal,
          dendrogram="none",
          trace="none",
          Colv=FALSE,
          Rowv=FALSE,
          margins=c(8,12))

11.9 Genes deregulated in Nicolai et al., 2006

11.9.1 List of the genes

sel1 <- c('AT2G03090','AT3G10950','AT3G25250','AT4G30280','AT5G13210','AT5G65110','AT1G12780','AT4G02520','AT3G12970','AT3G47540',
          'AT4G11650','AT4G30490','AT2G29490','AT2G38870','AT3G45970','AT5G22920','AT5G39320','AT1G75380','AT5G39580','AT5G57655',
          'AT1G54100','AT1G68440','AT1G76870','AT2G33150','AT3G04720','AT3G44300','AT3G59270','AT1G51400','AT2G30860','AT3G28180',
          'AT4G37610','AT5G07440','AT5G49360') 

11.9.2 Preparation of the expression table for the shortlisted genes

AvgTOR <- Avg[match(sel1,rownames(Avg)),]
SDTOR <- SD[match(sel1,rownames(SD)),]

11.9.3 Graphical representations

11.9.3.1 Combined barplots

barcenters <- barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = sel1)
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR-SDTOR, y1=AvgTOR+SDTOR,
       lwd=1.5, angle=90, length=0.05,code=3)
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

11.9.3.2 Separated barplots

for (i in 1:length(AvgTOR[,1])){
  barcenters <- barplot(AvgTOR[i,],beside=T, cex.names=0.7,legend.text = sel1[i], las=2)
  arrows(x0=barcenters, x1=barcenters, y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
         lwd=1.5, angle=90, length=0.2,code=3)
}

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

11.9.3.3 Individual graphs without colors

for (i in 1:length(AvgTOR[,1]))
{
  plot(AvgTOR[i,],ylim=c(min(AvgTOR[i,]-SDTOR[i,]),max(AvgTOR[i,]+SDTOR[i,])),
       xaxt="n",xlab="",ylab=sprintf("gene = %s",rownames(AvgTOR)[i]))
  axis(side = 1,at=1:13, colnames(AvgTOR),cex.axis=0.7,las=2)
  arrows(x0=1:length(AvgTOR[i,]), x1=1:length(AvgTOR[i,]),
         y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
         lwd=1.5, angle=90, length=0.05,code=3)
}

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

11.9.3.4 Individual graphs with colors

a <- matrix(NA, nrow=6, ncol=3)
colnames(a) <- c(0,6,24)
rownames(a) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
b <- matrix(NA, nrow=6, ncol=3)
colnames(b) <- c(0,6,24)
rownames(b) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")


for (i in 1:length(AvgTOR[,1]))
{
  a[1:6,1] <- AvgTOR[i,1]
  a[1:6,2] <- AvgTOR[i,2:7]
  a[1:6,3] <- AvgTOR[i,8:13]
  
  b[1:6,1] <- SDTOR[i,1]
  b[1:6,2] <- SDTOR[i,2:7]
  b[1:6,3] <- SDTOR[i,8:13]
  
  plot(colnames(a),a[1,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),ylab=rownames(AvgTOR)[i])
  lines(colnames(a),a[2,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),lty=2)
  lines(colnames(a),a[3,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise")
  lines(colnames(a),a[4,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise",lty=2)
  lines(colnames(a),a[5,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3")
  lines(colnames(a),a[6,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3",lty=2)
  
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[1,] - b[1,],
         y1=a[1,] + b[1,],
         lwd=1, angle=90, length=0.05, code=3)
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[2,] - b[2,],
         y1=a[2,] + b[2,],
         lwd=1, angle=90, length=0.05, code=3)
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[3,] - b[3,],
         y1=a[3,] + b[3,],
         lwd=1, angle=90, length=0.05, code=3, col="turquoise")
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[4,] - b[4,],
         y1=a[4,] + b[4,],
         lwd=1, angle=90, length=0.05, code=3, col="turquoise")
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[5,] - b[5,],
         y1=a[5,] + b[5,],
         lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[6,] - b[6,],
         y1=a[6,] + b[6,],
         lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
}

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

11.9.3.5 Heatmap

AvgTOR[AvgTOR == 0] <- 0.000001
AvgTOR_norm <- log2(AvgTOR[,] / AvgTOR[,1])
AvgTOR_norm[AvgTOR_norm < -3] <- -3; AvgTOR_norm[AvgTOR_norm > 3] <- 3


heatmap.2(AvgTOR_norm,
          col=hpal,
          dendrogram="none",
          trace="none",
          Colv=FALSE,
          Rowv=FALSE,
          margins=c(8,12))

11.10 Preparation of other lists

  • Preparation of the hexokinase list
sel1 <- c("AT1G05205","AT1G47840","AT1G47845","AT2G19860","AT4G29130")
  • Preparation of the AtHXK1
sel1 <- c("AT1G47845","AT4G29130")

12 Session Info

## R version 4.0.2 (2020-06-22)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.5 LTS
## 
## Matrix products: default
## BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
##  [1] grid      parallel  stats4    stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] jsonlite_1.7.1              vsn_3.56.0                 
##  [3] VennDiagram_1.6.20          futile.logger_1.4.3        
##  [5] tximport_1.16.1             forcats_0.5.0              
##  [7] stringr_1.4.0               dplyr_1.0.2                
##  [9] purrr_0.3.4                 readr_1.4.0                
## [11] tidyr_1.1.2                 tibble_3.0.3               
## [13] tidyverse_1.3.0             scatterplot3d_0.3-41       
## [15] RColorBrewer_1.1-2          plotly_4.9.2.1             
## [17] pander_0.6.3                magrittr_1.5               
## [19] LSD_4.1-0                   limma_3.44.3               
## [21] hyperSpec_0.99-20200527     xml2_1.3.2                 
## [23] ggplot2_3.3.2               lattice_0.20-41            
## [25] here_0.1                    gplots_3.1.0               
## [27] DESeq2_1.28.1               SummarizedExperiment_1.18.2
## [29] DelayedArray_0.14.1         matrixStats_0.57.0         
## [31] Biobase_2.48.0              GenomicRanges_1.40.0       
## [33] GenomeInfoDb_1.24.2         IRanges_2.22.2             
## [35] S4Vectors_0.26.1            BiocGenerics_0.34.0        
## [37] data.table_1.13.0          
## 
## loaded via a namespace (and not attached):
##  [1] colorspace_1.4-1       ellipsis_0.3.1         rprojroot_1.3-2       
##  [4] XVector_0.28.0         fs_1.5.0               rstudioapi_0.11       
##  [7] affyio_1.58.0          bit64_4.0.5            AnnotationDbi_1.50.3  
## [10] fansi_0.4.1            lubridate_1.7.9        splines_4.0.2         
## [13] geneplotter_1.66.0     knitr_1.30             broom_0.7.1           
## [16] annotate_1.66.0        dbplyr_1.4.4           png_0.1-7             
## [19] BiocManager_1.30.10    compiler_4.0.2         httr_1.4.2            
## [22] backports_1.1.10       assertthat_0.2.1       Matrix_1.2-18         
## [25] lazyeval_0.2.2         cli_2.0.2              formatR_1.7           
## [28] htmltools_0.5.0        tools_4.0.2            affy_1.66.0           
## [31] gtable_0.3.0           glue_1.4.2             GenomeInfoDbData_1.2.3
## [34] Rcpp_1.0.5             cellranger_1.1.0       vctrs_0.3.4           
## [37] preprocessCore_1.50.0  xfun_0.18              testthat_2.3.2        
## [40] rvest_0.3.6            lifecycle_0.2.0        gtools_3.8.2          
## [43] XML_3.99-0.5           zlibbioc_1.34.0        scales_1.1.1          
## [46] hms_0.5.3              lambda.r_1.2.4         curl_4.3              
## [49] yaml_2.2.1             memoise_1.1.0          latticeExtra_0.6-29   
## [52] stringi_1.5.3          RSQLite_2.2.1          highr_0.8             
## [55] genefilter_1.70.0      caTools_1.18.0         BiocParallel_1.22.0   
## [58] rlang_0.4.7            pkgconfig_2.0.3        bitops_1.0-6          
## [61] evaluate_0.14          htmlwidgets_1.5.2      bit_4.0.4             
## [64] tidyselect_1.1.0       R6_2.4.1               generics_0.0.2        
## [67] DBI_1.1.0              pillar_1.4.6           haven_2.3.1           
## [70] withr_2.3.0            survival_3.1-12        RCurl_1.98-1.2        
## [73] modelr_0.1.8           crayon_1.3.4           futile.options_1.0.1  
## [76] KernSmooth_2.23-17     rmarkdown_2.4          jpeg_0.1-8.1          
## [79] locfit_1.5-9.4         readxl_1.3.1           blob_1.2.1            
## [82] reprex_0.3.0           digest_0.6.25          xtable_1.8-4          
## [85] munsell_0.5.0          viridisLite_0.3.0